I am definitely not a qaualified expert to credit or discredit Japanese history, but I do know for a fact that Aikido and the Samurai are not directly related. Aikido was created after feudal Japan. It is a realtively new martial art. I doubt any true Samurai learned Aikido. And besides, Samurai fought for their lives, not spiritual enlightenment.

The difference shows clearly if you compare the "soft" Aikido sword with more traditional (and combat-oriented) kenjutsu schools with medieval/military roots, like Kashima or Tenshin Shoden KSR.
If you have the chance to look (and even better, train) at both, you will probably come to the conclusion that the former is an evolution of the latter, and that the former (Aikido sword) clearly doesn't fit a potential real battle situation; the latter are surely more geared toward effectiveness (and even brutality) rather than armony and circularity.
A 14-15th century samurai on the battlefield wouldn't handle a sword like a modern aikidoist does... he would have died as fast as he raised (too much) the sword to do shomen against the first decent trained enemy